hmmmm. Interesting thread. Not quite my situation, but....(Note: I have 2 identical motherboards, and they don't match, same bios and cards)
But thanks for that !
The only thing I can think of, is a BIOS setting somewhere.
If you haven't done so already, make sure the BIOS version of the boards are both the same as the one you currently have operating at 1x 16X and 1x 4X.
Next, reboot both machines and go over the BIOS settings line by line, section by section.
Note any descrepancy. I'm sure you thought to do all of this already, so I'm just thinking out loud here.
Make sure all external GPU power connectors are connected and providing sufficient power to the GPUs. I don't know how true this is, but I've read somewhere that if the GPU isn't getting enough juice, the mobo may reduce the PCI-e multi. I may be very wrong here so don't quote me. But try different power lines to the GPU. It can't hurt.
I don't know what else to do or try. I'd say it's a little easy to miss BIOS setting somewhere.
I'll look through the online PDF manual and see if I could spot anything obvious.
Keys
P.S. Sorry, but in my pre-coffee state, I was looking at the 965 DQ6.
Now that I've had my coffee, I'm noticing two board revisions for the P35 DQ6
Rev. 1.0
Rev. 1.1
I'm guessing only a BIOS difference separates the two shipping products.
http://www.gigabyte.com.tw/Products/Motherboard/Products_ComparisonSheet.aspx?ProductID=2637,2532
I'll go through this online PDF manual.